The m6A methyltransferase complex protein VIRMA engages hepatitis C virus RNA through a WTAP-independent mechanism

Cellular proteins in the m6A methyltransferase protein complex (m6A-MTC) work together to modify both cellular and viral RNAs with N6-methyladenosine (m6A), an RNA modification that regulates viral infection. We previously showed that hepatitis C virus (HCV), a cytoplasmic positive-sense RNA virus, has an m6A-modified RNA genome. We also found that m6A deposition on HCV RNA requires WTAP, which promotes association of the METTL3-METTL14 catalytic heterodimer to the viral RNA. However, the factors that directly recognize HCV RNA and recruit the m6A-MTC to the viral genome are unknown. Here, we identify the cellular m6A-MTC component VIRMA as an HCV RNA-targeting factor required for METTL3 association with the viral genome. We show that endogenous VIRMA can associate with both HCV and cellular RNAs independently of WTAP. Further, we define distinct domains of VIRMA involved in WTAP interaction and RNA binding and show that the regions of VIRMA involved in WTAP-interaction are required for cellular but not HCV RNA association. Together, these results establish that VIRMA uses distinct molecular determinants to engage viral and cellular RNAs and define VIRMA as a substrate-recognition factor required for m6A-MTC association with HCV RNA.